My first question is if anyone knows why this is happening and secondly,

I can still look at the tabular file though for the differential gene expression testing and it still has all the genes and if they are significant or not and their calculated FPKM values? Can I still trust that?

Hi Val,
Are you setting a 'library type' in Cuffdiff? A similar error was reported on BioStars (https://www.biostars.org/p/118904/) and setting the 'library type' in Cuffdiff fixed the issue in that case.

If I run HISAT without assigning the 'specify strand specific information' and run Cuffdiff on the output I get the same error you are seeing. When I run HISAT and assign the correct 'specify strand specific information' parameter, I no longer see errors.

Thanks for all the suggestions! I'm not sure why this keeps happening. I had originally uploaded the bam files directly after aligning the data locally.
Having uploaded the fastq files and aligning within galaxy has made the error disappear even though all of the parameters are the same. No idea why this might be happening, hopefully Jen might be able to let us know.